You are referring to crosstalk. This only occurs when a button is pressed on both remotes at the same time (I assume this is what you meant when you said both rooms being used at the same time). Even of you assign different IR ports, crosstalk issues can still occur.

The OP stated that his base stations were on different frequencies. That is not true. Unless he has a regular series in one room (418 MHz) and an i series in the other (433 MHz) then he has them on the same frequency. What he is referring to is the RF IF which is simply a different channel set physically on the base and remote in programming. Crosstalk will occur across different RF IDs. Having an i series in one room and a regular in the other should eliminate that problem.

In this case though, it appears the issue was simply due to a miswire which has been corrected.